


Beneath Still Waters Lie (The Depths of My Desperation)

by sourdough_pup



Category: Agents of S.H.I.E.L.D. (TV)
Genre: AU--Jemma was never on the Bus, Established Relationship, F/M, Kidnapping, Non-Consensual Drug Use, Truth Serum, married au, post season 1 AU
Language: English
Status: Completed
Published: 2015-08-10
Updated: 2016-04-11
Packaged: 2018-04-14 01:18:53
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 4,149
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4544619
Author URL: https://archiveofourown.org/users/sourdough_pup/pseuds/sourdough_pup
Summary: <blockquote class="userstuff">
              <p>When SHIELD falls, a brief phone call is enough to reassure Jemma that her husband is safe. As weeks go by and she doesn't hear from him or anyone else, she gets a bit desperate.</p>
            </blockquote>





	1. denial (you’re never desperate until you are)

Jemma was on leave when SHIELD fell. She had taken a week and a half to attend her favorite cousin’s wedding and her mother’s birthday, hoping to be able to catch up with her husband for her last few days if his team wasn’t halfway around the world again. She had barely caught a glimpse of the story on the news before her phone began to ring. Still watching the TV, she didn’t even look at the caller ID before she answered. “This is Jemma.”

“Oh thank god,” She could hear the relief in Grant’s voice. “Where are you?”

“I’m at home, for the wedding,” she reminded him, the tension that had filled her barely fading as she muted the TV, then asked. “Where are you? Are you alright? I just saw the news, what’s going on?”

“I’m fine,” he reassured her. “We’re headed for the Hub. Garrett and Trip are with us, so we should be ok, even if HYDRA is there. I…the Sandbox fell. I know they went after the Academy, but we haven’t heard word yet about the outcome. The Fridge is ours. The Triskelion was destroyed, but they took out the Helicarriers, so I’d call that a win. The Cube and the Treehouse—“

“I didn’t ask for a rundown on the bases, I asked about you. What aren’t you telling me?” Jemma interrupted.

“Sorry, I was just worried. When we heard the Sandbox fell…I forgot you took that leave.” He explained.

“I know you worry, Grant, but you’re deflecting. What’s wrong? Please, just tell me.” Jemma begged, her own concern growing.

Grant’s exhale was audible even over the phone. “We were attacked; both the Bus and Garrett’s plane. We took care of it, but we’re being pulled into the Hub.” Jemma heard what he didn’t say: if they were being forced to the Hub, it was very possible HYDRA had taken it and was bringing them in to remove them as a threat.

Jemma’s own exhale was shaky. “I see.” It wasn’t as if she wasn’t used to her husband going into dangerous, unknown situations; he was a Specialist, it was in the job description. She took a deep breath and forced herself to stay calm. “Do you have a plan?”

“We do,” Grant’s voice was steady. If he didn’t want her to know he was lying, she would never be able to tell, but she had decided to trust him to tell the truth when they got married. “We’ll be alright, Jem, I just needed to know that you were safe.”

“I am,” she promised him. “I’ll keep my gun on me and my guard up, I promise.”

“Good,” Grant said, “I’ll—“ she could hear other voices calling over the phone. “I’ve got to go, but I’ll check in. I love you.”

“I love you, too. Stay safe.” She sat, breathing deeply for a few moments before she turned the sound back on. She watched the news with the knowledge of an insider, pulling it and what Grant had told her together. She took one last, deep breath, before heading to her room. Grant promised to contact her, but she had a few other things to take care of.

The rest of the week passed in a blur. Jemma made phone calls and searched for friends and colleagues, to only partial success. Many of those she tried didn’t answer, some had survived and left SHIELD, and yet others answered with “Hail HYDRA.” The worst part, though, was that Grant had stopped texting her after five days. When another week passed with no contact from Grant or anyone else from SHIELD, she decide to take matters into her own hands.

None of her research yielded anything on Grant’s team—which was telling in and of itself. Many SHIELD agents had publicly been arrested or joined other organizations; most of the dead had been found and their families notified by the local government. The lack of information meant they had either been captured or were in hiding. Luckily, Maria Hill, former Deputy Director, was very easy to find, and if anyone knew what happened to Coulson and his team, it was her. She was also easy to get in touch with if you knew what you were doing.

Another week of emails and phone calls and she was walking into a small New York café where Hill was waiting at a table. Quickly ordering a small hot chocolate rather than risking badly made tea, she approached the table. Taking the offered hand when Hill stood, she smiled stiffly in greeting. “Thank you for meeting me, ma’am.”

“It wasn’t a problem.” Hill replied, gesturing for her to sit before taking her own seat. “It was nice to get out of that Tower for a bit. How can I help you?”

Pleasantries out of the way, Jemma got straight to the point. “Have you had any contact with Coulson or his team?”

Hill didn’t look very surprised by the question, and it was likely that she had anticipated the reason for the meeting. “I have, actually. They all survived and were pursuing a few things when we spoke.”

“They’re all ok? Then do you know how I can contact them? Grant stopped texting me over two weeks ago and I—“ Jemma cut herself off, taking a deep breath; Hill didn’t need to listen to her panic.

“Agent—Dr. Simmons,” Hill said, voice uncharacteristically gentle, “Ward is HYDRA.”

“No,” Jemma protested reflexively, “Grant would never…” She trailed off as Hill shook her head.

“I’m sorry, Simmons. I’ve seen the NSA footage of him leading the attack on the Fridge myself. Garrett recruited him before he was even a SHIELD agent.”

“I see,” Jemma responded, voice weak as her head spun, holding onto her mug like a lifeline. Her husband was every inch a specialist—all the bad that went with the good—but… "You said Garrett recruited him. Garrett is HYDRA, too?” She followed Maria’s comment to the only obvious conclusion, grasping for an explanation.

“Was. He’s dead now.” There was clearly a story Hill wasn’t sharing; Jemma suspected it had to do with who killed him. Based on the lengths Jemma had had to go to find anything, the fact that Hill worked for Stark now, and the lack of details on what happened to Coulson’s team, she suspected it had to do with the future of SHIELD.

Jemma’s genius was usually applied to science, but that didn’t mean she couldn’t apply it to other concepts. Hill’s evasiveness and the lack of contact from her husband or her husband’s team (which included one of her oldest friends) meant SHIELD was up to something, but she wasn’t invited. Given Grant’s supposed status as a HYDRA traitor (and she would need to check out those tapes herself; it wasn’t that she though Hill would lie, but this was her husband they were talking about), she inferred that she was no longer trusted due to their connection. At least he wasn’t dead; Hill would have come out and told her, rather than talking around it if that had been the case.

“Well,” she said finally, nodding respectfully to Hill. “Thank you for being honest with me. Now that SHIELD has fallen, I suppose I had better start looking for a new job. Let me know if you need anything, and if you hear from Fitz, would you pass on my information?” She asked, holding out a few business cards (the non-SHIELD ones Grant had helped her make, “just in case”) as both women stood up from the table.

Maria took them gracefully, then shook her hand again. “I will. Good luck with your search, Dr. Simmons, not that you’ll need it.”

“I appreciate the sentiment,” Jemma told her with a smile, “Now, if you’ll excuse me?” At Hill’s nod, Jemma left the cafe, walking briskly to hail a cab. It was a little offensive that they thought she might be HYDRA simply because her husband was, but she couldn’t blame them for their paranoia. It just meant she would have to take care of things herself.


	2. haze (desperate times call for desperate measures)

**Notes for the Chapter:**

> Warnings at the end of the chapter (concerning non-consensual drug use).

Skye peered through the smoke and dust at the rubble that remain. They had just gotten wind of the small HYDRA lab the day before, then found it blown to pieces the next morning. Concerned, Coulson had ordered her to sort through the salvaged computers and electronics for any clues about what HYDRA was doing. Fitz had helped her find everything with his DWARFs after Hartley’s team had cleared the area, but with so few agents, Skye was on her own for the rest. With one last glance, she settled in to work

After an hour, Skye had to get up and stretch. So far, her search had been fruitless, unless an order for 50 boxes of medium sized latex gloves was integral to HYDRA’s next attack. She doubted it. Walking around, she tensed, hand going to her gun, when she heard noise from the drive.   
Ducking behind what was left of a wall. She watched as a car pulled up and a woman about her age got out.

“Hello? Is anyone there?” The other woman called out. “I saw smoke from the road, does anyone need help?” She hurried towards the wreckage as she pulled out her phone.

A concerned citizen was something Skye could deal with; explaining how the cops got involved to Coulson was not. She stood. “Hey,” she called out with a friendly smile, walking towards her. “Sorry, I didn’t hear you drive up.” Skye lied.” Agent Skye, FBI.” She offered, pulling out the fake ID Hunter had made.

“Oh, thank goodness!” the woman sighed, peering at the badge before straightening up and offering her hand. “Dr. Jemma Simmons. Is there anything I can do?” She asked as they shook hands, before quickly assuring Skye, “Not that you need it, I’m sure, but I have to at least offer.”

“Not unless you’re familiar with the area, Dr. Simmons?” Skye asked, only for Simmons to shake her head and mumble about just passing through. “Then thank you, but you’re right, I’m—whoa!” Sky exclaimed as the world spun around her.

“Agent Skye?” The doctor grasped her elbows to help her stay upright. “Are you sure you’re ok? Here, sit.” She helped Skye over to her car, checking her pulse and peering into her eyes, before Skye lost consciousness.

–

“Oh, good, you’re awake.” Skye heard as she became aware of her uncomfortable position and the ache in her head. She tensed as she recognized the feeling of handcuffs and opened her eyes to see the doctor from before.

“Who are you and what do you want with me?” Skye spat out.

“I told you,” the woman said, “I’m Dr. Jemma Simmons, but I suppose you’re right, I did mislead you. I’m a little surprised you didn’t recognize   
me, I’ll have to have words with Grant.” She seemed to muse to herself. “Agent Jemma Ward might be a little more relevant.”

Skye froze. She did know that name. Ward had mentioned being married, but didn’t really talk about his wife much and she’d never gotten a   
chance to see a picture, let alone meet her. Given the situation, she was beginning to wish it had stayed that way.

Jemma obviously noticed. “Relax, Agent Skye. I’m not going to hurt you.” She scolded.

Skye scoffed. “Yeah, right. I have enough experience to know that HYDRA’s MO generally includes lots of pain.”

The female Ward had the nerve to look offended. “I am an Agent of SHIELD, I would never work for HYDRA!”

“You knocked me out, kidnapped me, and have me tied to a chair. Excuse me if I don’t take your word for it.” Skye told her.

“I just want to know what happened to Grant!” Jemma cried out, clearly frustrated. Skye bit back a smile. She may not be a specialist, but she thought she was handling herself fairly well. She watched as her captor took a deep breath and appeared to calm herself. “Please, can you tell me where he is? Or if he’s even alive?”

“What makes you think I even know?” Skye asked, feeling at her bonds to see if she could free herself.

Jemma sighed. “We did talk, you know. He told me about his team. When HYDRA…happened, he was with you. I looked into it, and I couldn’t find anything mentioning him. And there were no records anywhere about your team. I drew my own conclusions, and you haven’t exactly denied it.”

“You know what they say about assuming.” Skye couldn’t help herself, but knew Jemma was right. She’d never believe Skye didn’t know now. “But even if I do, I’ll never give you anything.”

“Very well. If you won’t just tell me, perhaps some encouragement is necessary.” Jemma said, as she picked up a syringe off the table  
Skye laughed. “Nice try, but your husband already told me there’s no such thing as a truth serum.”

Jemma smiled tightly at her. “My husband is very good at what he does, but he doesn’t know everything. As a matter of fact, I managed to perfect the formula just before HYDRA came out. For what it’s worth,” she said calmly as Skye began to struggle in earnest, “I’ve been told it’s quite pleasant, a rather relaxing experience.”

This time, Skye felt the pinch of a needle and rather than passing out, she felt like she was floating. When Jemma asked her questions this time, she found herself spilling what she knew. She managed to control herself enough to give minimal answers, but Jemma was thorough, asking question after question, not just about Ward, but about the new SHIELD, Coulson and the team, codes, and more.

Finally, finally, she stopped. “Thank you, Skye,” she said, smiling brightly. “You’ve been very helpful. I need to speak to Coulson, but I’m sure he’ll be reasonable, and then you can go home.”

–

Coulson frowned at the incoming video call. An unknown number was never something people wanted to see, but especially while working for secret organizations. Waving Fitz and May out of sight, he tapped to answer.

“Director Coulson!” A smiling Jemma Ward was just about the last person Coulson expected. “Congratulations on your promotion. How are things going?”

“Agent Simmons,” Despite being married, Jemma usually went by her maiden name, to reduce confusion she had always claimed. “Thank you. I’m quite well. And you?”

“I’m about as well as can be anticipated, considering SHIELD fell, my husband is missing, and I’ve had to rebuild my life from scratch.” She answered politely. “How is the rebuilding going? I don’t suppose you’re looking for a biochemist?”

Coulson smiled, but mentally gave her the point. “It’s slow going. We’ve got a pretty good science team, but I’ll let you know if that changes.”

“Wonderful,” she replied. “In the meantime, I’d like to speak with Grant, please.”

Coulson frowned. She wasn’t asking if they knew where her husband was, but spoke of his location like fact. She definitely wasn’t supposed to know that. She also wasn’t supposed to have his number, though, so maybe he could figure out where she got her information. “I’m afraid I can’t help you with that. I haven’t seen Ward in some time. He is HYDRA, you know.”

Jemma sighed as if put out. “Yes, I had figured that much out. He always was too loyal to Garrett. But you can help me speak to him. You’re welcome to monitor the conversation, of course, but if you could bring the tablet to Vault D, I would appreciate it.”

“Very well,” Coulson finally agreed after a long glance with May and Fitz. Hopefully, Fitz could trace her location while May investigated what she’d been up to. “If you will follow me,” he joked lightly as he picked up the tablet. “So Agent Simmons, care to tell me where you got your information?” He asked as he walked; direct was always a good route with her.

He could hear the smile in her voice as she answered. “Not at the moment, I’m afraid. Once I’ve spoken with Grant, though, I’d be happy to tell you.”

Thankfully, it was a short walk to Vault D from where he’d been meeting in the lab with May and Fitz. “Here we are. Good morning, Ward,” he addressed the specialist who was standing in the center of the cell. “You have a visitor, as it were.” He angled the tablet so the couple could see each other.

“Jem,” the man breathed out, surprise clear on his face.

“Hello Grant,” Coulson could hear the tears in her voice. A pang of guilt hit him. Jemma Simmons had been a good agent and everyone who knew her agreed the chances of her being HYDRA were practically nonexistent, but based on their marriage, he had ordered her kept in the dark about everything—cut off from SHIELD as if it had truly fallen--just in case. “How have you been?”

Even knowing how good Ward was, Coulson suspected the softening of his expression was genuine. “Not too bad. A bit bored, but I’ve been in worse situations. You holding up?”

“I’ve been better.” She admitted. “I miss you, even if you are a traitor.”

Grant shrugged. “I’d say I’m sorry, but…”

“I don’t expect you to. Though I have to ask, without Garrett, could I convince you to quit, maybe join a private company if SHIELD won’t take you?”

“It’s possible.” Grant grinned outright, and it only widened when he caught the frown on Coulson’s face. “There might be some negotiation required, but I’m sure we could agree to something.” 

“That will have to do. I’ll see you soon, darling.” Jemma’s voice changed, became more formal. “Director Coulson, how would you feel about a trade?”

Coulson instantly stiffened, even as Ward’s interest visibly peaked. “What kind of trade?” He asked. “And are you finished speaking with your husband or do we need to remain here?”

Jemma hummed. “Let’s stay here for now. As for the trade, you asked earlier how I knew where Grant was. Agent Skye was very helpful, and now I was hoping I could trade her for access to Grant.”

Ward immediately laughed as Coulson turned the tablet so he was facing the video, truly angry for the first time in the conversation. “What have you done to her?” He demanded.

“Nothing too terrible.” Jemma claimed. “I admit, espionage is not my forte, but the worst I did was knock her out with a sedative. You can see for yourself.” She moved so he could see Skye tied to a chair. She was bound and gagged, but looked furious rather than pained. “I managed to develop a truth serum of sorts, so she was more than happy to answer my questions.”

“You said it yourself, you’re not particularly skilled at espionage, so what makes you think we won’t just find you.” Coulson pointed out.

“I’m a terrible liar, but an excellent planner. I assume Fitz and May are tracking me?” She nodded as his frown deepened. “They’ll find me of course, but by the time they do, we will be gone and I will have moved on to plan B. I’ve never met him myself, but I believe the woman named Raina knows Skye’s father. I’m sure they would be more than willing to help me in return for Skye.” Coulson sucked in a breath, the threat clear. Jemma smiled at him. “I’d rather not, but I will if I have to. Besides, I’m not asking for you to release him. I am still loyal to SHEILD, even if it isn’t loyal to me. I’d come to you, though with a few contingency plans to make sure you don’t just throw me in my own cell. What do you say Director, do we have a deal?”

After long minutes, Coulson nodded. “We have deal. Do you need transport?”

“That won’t be necessary. You can expect us first thing tomorrow morning. Please remind your people not to shoot. You really won’t like the consequences if you do.” She told him before shutting off the connection.

“I really appreciate this—“ Coulson slammed his hand down on the controls to cut Ward off. He had a team to brief.

**Notes for the Chapter:**

> The drug use mentioned has two parts: first, Jemma gives Skye a sedative to kidnap her, then she gives her a truth serum to get information
> 
> I wrote this about 3 months ago. At the time, I started the third part, but it has been a struggle to write. It is about halfway done and while I'm trying to work on it, it's slow going, so don't expect it particularly soon.


	3. Everything is fine (Until the bitterness sets in)

There were two agents waiting at the door when Jemma pulled the car up to the entrance of the Playground. She smiled when she recognized Tripp as one of them, though was a little surprised Coulson hadn’t sent May. Parking, she got out and went to let Skye out as well, calling a greeting to the agents waiting, which wasn’t returned. Opening Skye’s door, she paused and looked at the waiting agents. “Agent Triplet, could you assist me with Agent Skye, please? She should be fine, but I had to give her a sedative earlier and I would hate for her to get injured if it hasn’t quite worn off yet.” Jemma requested. Tripp hesitated, but joined her, helping Skye out as Jemma undid the restraints and grabbed her bag out of the back. “Thank you. Shall we go inside?” 

She wasn’t expecting an answer as no one had spoken yet, on Coulson’s orders she suspected, so she was surprised when Tripp, still supporting Skye, smiled and offered, “After you.”

Jemma checked her bag, then proceeded through the door the other agent held open. “Thank you,” she told him as she passed him. Once inside, the other agent whose frown had yet to abate, took the lead, deftly guiding them through the many hallways to where Jemma assumed Coulson was waiting. As they walked, she saw many faces, both familiar and unfamiliar, most filled with distrust. She held her head high and kept walking; it was their unfounded lack of faith that had made her actions necessary. 

Finally, they arrived at Coulson’s office. Waiting with him were Fitz and May. Jemma forced herself to keep her expression pleasant. While she understood Coulson’s reasons and had never met May herself, Fitz was one of her oldest and closest friends and his silence had hurt. “Director Coulson, Agent May, Fitz.” She said with a polite smile and nod to each. “Thank you for accommodating me. As you can see, Agent Skye is doing well.” 

“Agent Simmons.” Coulson replied. “I appreciate that you were willing to resolve things so quickly and peacefully.”

Jemma raised her eyebrow at his statement, but decide not to remind him that it was his actions that caused the whole mess. No need to antagonize, now that she was this close.  
“Of course. As I told Agent Skye, I remain loyal to SHEILD.” Though Coulson and May didn’t react, Fitz’s wince was gratifying. 

“Indeed,” Coulson seemed as unwilling to cause a fuss as she was. “Now, I assume you are eager to see your husband, but there are a few things to handle go over we can let you into Vault D.”

“I agree,” Jemma said. From the raised eyebrows her statement got, she presumed they thought she would demand to see Grant immediately. As it was, she had a few things she wanted to discuss as well. “Why don’t you begin?”

Negotiations took nearly two hours, which was less then Jemma expected, though taking her own truth serum likely sped things along. In the end, Jemma was granted a supervised visit with Grant. She was more than willing to offer Grant the chance to use the truth serum to earn privileges, though she refused to let Coulson force it on him. She used it on herself to prove her intentions didn’t include freeing her husband, but made a point of reminding them of the connections she’d developed and precautions she had in place to make sure she would be able to leave unhindered. 

She doubted she would ever be an official member of SHIELD again, but for now she had enough. Time with her husband, a chance to see some old friends (even if they didn’t seem to care as much about her), and a rather petty feeling of vindication. 

When they finally allowed her into Vault D, it was with a number of instructions and a time limit. The wall containing Grant was opaque and they activated the secondary wall before disabling the first. They must have briefed Grant because he remained on the far side of the now deactivating wall as Jemma crossed over. He caught her in a kiss as she threw herself at him, relaxing into his arms even as the wall flickered back into existence. 

Eventually they separated but neither truly let go. Grant kept both hands on her hips while she tucked her own into the back of his waistband. 

"Hello husband." Jemma greeted him as she had after every long separation.

Grant's slow smile said he remembered. "Hello wife." 

**Notes for the Chapter:**

> It's finally done! Thanks to everyone who stuck with me. I'm so sorry it took so long. The ending is pretty ambiguous because everything I tried felt wrong, so feel free to imagine exactly how things go.


End file.
